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- PDB-7d89: Crystal structure of an inactivated double mutant (E182AE280A) of... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7d89 | ||||||
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Title | Crystal structure of an inactivated double mutant (E182AE280A) of a novel thermostable GH10 xylanase XynA | ||||||
![]() | Beta-xylanase![]() | ||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xie, W. / Yu, Q. / Wang, C. | ||||||
![]() | ![]() Title: Insights into the Catalytic Mechanism of a Novel XynA and Structure-Based Engineering for Improving Bifunctional Activities. Authors: Xie, W. / Yu, Q. / Zhang, R. / Liu, Y. / Cao, R. / Wang, S. / Zhan, R. / Liu, Z. / Wang, K. / Wang, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105 KB | Display | ![]() |
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PDB format | ![]() | 63.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7d88C ![]() 1v0lS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 49806.918 Da / Num. of mol.: 1 / Mutation: E182A, E280A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.55 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 24% PEG 600, 0.1M CaCl2, 0.1M MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.89→49.28 Å / Num. obs: 12123 / % possible obs: 99.56 % / Redundancy: 25.5 % / Biso Wilson estimate: 66.2367949314 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.021 / Rrim(I) all: 0.108 / Net I/σ(I): 34 |
Reflection shell | Resolution: 2.894→2.997 Å / Rmerge(I) obs: 0.108 / Num. unique obs: 12123 / CC1/2: 1 / Rpim(I) all: 0.021 / Rrim(I) all: 0.108 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1V0L Resolution: 2.89384086853→49.2798077289 Å / SU ML: 0.397124008712 / Cross valid method: FREE R-VALUE / σ(F): 1.37753762711 / Phase error: 28.1305524779 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.640519927 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.89384086853→49.2798077289 Å
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Refine LS restraints |
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LS refinement shell |
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